When the New York City Council announced this week that it had reached a deal on a sweeping zoning reform, the agreement was hailed as a major victory, a linchpin to achieving Mayor Bill de Blasio’s goal of building 80,000 units of affordable housing.

But one stubborn obstacle went unmentioned: The zoning change was meant to work in tandem with a key property tax exemption that no longer exists and can be resurrected only by the State Legislature. Without the tax break, known as 421-a, New York City may have to spend more to subsidize affordable housing, or risk allowing Mr. de Blasio’s housing target to go unmet.

The zoning change, called mandatory inclusionary housing, requires that the developers of rental apartment buildings in some parts of the city set aside a portion of units to be offered to tenants at below-market rates. Conceived when the 421-a exemption still existed, the change was expected to clear the way for the creation of about 12,000 affordable apartments through 2024, a sizable step toward the mayor’s goal.

Without the exemption, many in the real estate industry and the government believe that the impact of the zoning change will be seriously dampened.

“It is a strange moment,” said Benjamin Dulchin, executive director of the Association for Neighborhood and Housing Development, an advocacy group, which pressed the city to alter the zoning proposal to spur the creation of more units affordable to people at very low income levels. The exemption “was baked into all their assumptions about how neighborhood real estate markets would work and therefore how they would structure their mandatory inclusionary program.”

The exemption expired in January amid bitter squabbling between City Hall and Albany, and appears unlikely to be revived anytime soon.

David G. Greenfield, a councilman from Brooklyn who leads the body’s land use committee, said planners had considered 421-a so integral to the zoning change proposal that the exemption was “mentioned 438 times, by my count,” in a consultant’s report on the subject.

“There’s no question that 421-a plays a critical role and certainly the premise of M.I.H. was that there would be 421-a,” Mr. Greenfield, a Democrat, said, using a shorthand for the zoning proposal. “M.I.H. still works without it, but it doesn’t work as well.”

In the two years since Mr. de Blasio, a Democrat, took office in January 2014, developers have received construction financing for 13,929 affordable units, according to data from the Department of Housing Preservation and Development. Of those, 5,006, or more than a third, were to receive a 421-a subsidy, a clear sign of how heavily the mayor’s overall program relied on the now-defunct exemption.

Meredith Marshall, managing partner and co-founder of BRP Development, a company that builds both affordable and market-rate housing, said his company had rushed to start at least one project last year before the 421-a program expired. But the firm was unable to move quickly enough to begin a second one, on a parcel in central Harlem where BRP had planned a medium-size building with fewer than 50 rental units. As a result, Mr. Marshall said, the company was considering a nonresidential use for the site.

Though the project might have included fewer than 10 affordable units if it had proceeded, its demise shows how the lack of 421-a subsidies could steadily undermine the mayor’s housing goals.

“Would I prefer to have 421-a? Absolutely,” said Vicki Been, commissioner of housing preservation and development. “But does it mean the mayor’s housing plan is doomed? No. It will require us to be more creative and more nimble.”

Ms. Been believes state lawmakers will eventually revive the tax break. Even without it, she said, the city could still meet the 12,000-unit goal connected to the rezoning by using other tax-abatement programs and city subsidies, though some officials contend that doing so could divert part of the $8 billion the city has earmarked for meeting the mayor’s housing goals.

At the same time, Ms. Been acknowledged that it would be harder to deliver the full results envisioned under the zoning change without the tax abatement.

“You’re working without one spark plug so you’re not running at full throttle,” she said.

She cited an internal study that estimated that 60 percent of the affordable units that began construction over the past two years and were eligible for the 421-a program might have qualified for a different sort of abatement.

But because the other types of subsidies were geared toward developments that were either entirely affordable or subject to other stringent requirements, it was unclear whether developers of similar projects would seek to use them or would simply choose to build condos instead of rental housing, which is the trend in many areas of the city.

“Our position is one of watchful waiting,” Mr. de Blasio said in a recent interview. “People are now getting used to the fact it’s not there. I think for a lot of people that’s discomfiting and that may create some of the good pressure toward a solution.” In addition to the new construction, the mayor’s plans call for keeping 120,000 units that are currently affordable from reverting to market rates.

The exemption was popular with the real estate industry, but reviled by housing advocates, who saw it as a giveaway to some of New York’s wealthiest developers and a highly inefficient means of creating affordable housing.

Last summer, with the 421-a program set to expire unless the Legislature renewed it, Mr. de Blasio proposed a revised version that sweetened the subsidy for developers in exchange for the creation more below-market units

But Gov. Andrew M. Cuomo, a Democrat who has been feuding with the mayor over various issues, sided with labor unions that insisted the program include a provision requiring projects receiving subsidies to pay union-level wages, something that developers and the mayor said would make such projects too costly. The Legislature passed a six-month extension and called on the real estate industry and construction unions to reach a deal on wages that would allow the abatement to continue. But the two sides could not agree and the tax abatement died on Jan. 15.

City officials, citing a rise in construction permits before the exemption expired, said the loss of the program would not be felt right away because there were plenty of affordable units being built. Other data provided by the city does not support that contention.

Of the affordable units to get 421-a subsidies over the last two years, fewer received construction financing through the city last year than in 2014 — 2,406 compared with 2,600, a 7 percent decline at odds with the idea that there was a rush to build as the deadline approached. City officials said the data may not reflect some 421-a projects.

Jordan Barowitz, a spokesman for the Durst Organization, a large developer, said the second phase of a 2,400-unit rental complex called Hallets Point that the company is building in Astoria, Queens, was in jeopardy if the 421-a program was not revived.

“The economics of the project are simply not viable” without the subsidy, he said. “We will lose more than 300 affordable units if we can’t proceed.” The Hallets Point project is not affected by the zoning change, which the Council is expected to vote on next week.

John Banks, president of the Real Estate Board of New York, which represents large developers, said it was not feasible to build rental housing in New York City without the 421-a subsidies. The combination of high construction and land costs and high taxes on rentals made such construction unprofitable, he said, and the passage of mandatory inclusionary housing would not change that.

The subsidies are “the linchpin in meeting the goal,” Mr. Banks said. “Without 421-a, in a lot of the city it’s going to be hard to fulfill the provisions of M.I.H.”

Mr. Greenfield, the city councilman, said that approving the zoning change could force the Legislature to restore some version of the exemption.

“That will put more pressure on Albany to act,” he said. “It will be very clear and very stark that the lack of 421-a is what’s preventing us from developing more affordable housing in New York City.”

A version of this article appears in print on , Section A, Page 20 of the New York edition with the headline: End of Subsidy May Threaten Impact of Shift in City Zoning. Order Reprints | Today’s Paper | Subscribe